diff options
| -rwxr-xr-x | quikr.py | 13 | ||||
| -rwxr-xr-x | quikr_train.py | 13 |
2 files changed, 22 insertions, 4 deletions
@@ -4,13 +4,14 @@ import sys import scipy.optimize.nnls import scipy.sparse import numpy as np +import quikr_util as qu from subprocess import * import argparse import platform +import gzip def main(): - parser = argparse.ArgumentParser(description= "Quikr returns the estimated frequencies of batcteria present when given a \ input FASTA file. \n \ @@ -44,12 +45,20 @@ def main(): lamb = args.lamb xstar = quikr_load_trained_matrix_from_file(args.fasta, args.trained_matrix, args.kmer, lamb) + np.savetxt(args.output, xstar, delimiter=",", fmt="%f") return 0 def quikr_load_trained_matrix_from_file(input_fasta_location, trained_matrix_location, kmer, default_lambda): - trained_matrix = np.load(trained_matrix_location) + if qu.isCompressed(trained_matrix_location): + print "compressed!" + trained_matrix_file = gzip.open(trained_matrix_location, "rb") + else: + trained_matrix_file = open(trained_matrix_location, "rb") + + trained_matrix = np.load(trained_matrix_file) + xstar = quikr(input_fasta_location, trained_matrix, kmer, default_lambda) return xstar diff --git a/quikr_train.py b/quikr_train.py index 5089e2a..a427436 100755 --- a/quikr_train.py +++ b/quikr_train.py @@ -2,6 +2,7 @@ import numpy as np import os import sys +import gzip from subprocess import * import platform import argparse @@ -19,7 +20,10 @@ def main(): parser.add_argument("-i", "--input", help="training database of sequences (fasta format)", required=True) parser.add_argument("-o", "--output", help="sensing matrix (text file)", required=True) - parser.add_argument("-k", "--kmer", type=int, help="kmer size (integer)", required=False ) + parser.add_argument("-k", "--kmer", help="kmer size (integer)", + type=int, required=False ) + parser.add_argument("-z", "--compress", help="compress output (integer)", + action='store_true', required=False) args = parser.parse_args() @@ -29,7 +33,12 @@ def main(): # call the quikr train function, save the output with np.save matrix = quikr_train(args.input, args.kmer) - np.save(args.output, matrix) + if args.compress: + output_file = gzip.open(args.output, "wb") + else: + output_file = open(args.output, "wb") + + np.save(output_file, matrix) return 0 |